A genome assembly of the Atlantic chub mackerel (Scomber colias): avaluable teleost fishing resource.

Miguel Santos,André M Machado,Ana Veríssimo,L Filipe C Castro,Elsa Froufe,Mónica Felício,Filipe Salvador-Caramelo,Miguel M Fonseca,Rute R Da Fonseca,Marcos Domingues,Raquel Ruivo,André Gomes-Dos-Santos,Nélson Alves,Ricardo Capela

doi:10.46471/gigabyte.40

Abstract

The Atlantic chub mackerel, Scomber colias (Gmelin, 1789), is a medium-sized pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance, being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S.colias, produced with PacBio HiFi long reads and Illumina paired-end short reads. The estimated genome size is 814 Mbp, distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4.19 and 3.34 Mbp, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3% of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this genome assembly ranks fourth in high-quality genome assemblies within the order Scombriformes and first in the genus Scomber.

Highlights

The frozen tissue was shipped to Brigham Young University DNA Sequencing Center (BYU), where genomic DNA (gDNA) with high molecular weight was extracted from 1.1 g of muscle using the QIAGEN Genomic-tip 20/G kit
The quality and concentration of the gDNA were assessed with Qubit Fluorometric system (ThermoFisher), and the fragment size was determined with a fragment analyser (Agilent Technologies, RRID:SCR_013575) before loading on the Pacbio Sequel II system (PacBio Sequel II System, RRID:SCR_017990)
When gene names were not retrieved from S. colias genome annotation, further TBLASTN searches were performed in the primary genome assembly with optimised parameters (-max_hsps 1 to keep the best query-subject pair), using D. rerio sequences as a query

Summary

Introduction

The scaffolded genome and the long-read assemblies, initially produced by Hifiasm and HiCanu and discarded based on contiguity and completeness, were inputted to Cobbler v.0.6.1 [36] and RAILS v.1.5.1 [36] pipeline, with default parameters. The liver RNA-Seq reads (accession number: SRR6367407 [10]) were downloaded, mapped against the S. colias genome assembly using Hisat2 v.2.2.0 [39, 40] with default parameters, and converted to BAM and sorted files using Samtools v.1.9 (SAMTOOLS, RRID:SCR_002105) [49].

Results

Conclusion